Development of a “Realistic” Model of the Dynamic Chromatin Fiber using an Integrated Computational Approach

Abstract

DNA in eukaryotic cells is highly compacted into a hierarchical chromatin structure to fit inside the nucleus. Linker histones play an important role in this packing. Their interaction with the nucleosomes and intervening DNA linkers, in combination with linker length, are believed to affect chromatin folding and long-range interactions. The details of chromatin structure at this level of compaction are still an open question but have profound implications on biological processes, such as gene expression. Two major challenges are that linker histones contain a long intrinsically disordered C-terminal domain (CTD) and determination of high-resolution structures of chromatin has not been possible due to the large size of the system and its dynamic nature.We are taking advantage of the recently published 11-A resolution electron microscopy maps of two chromatin fibers (Song et al., 2014), to construct a complete low-resolution model of chromatin. High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes new DNA optimization methods. Situs is used to score all models against the density maps. Linker histones are modeled on the densities extracted after accounting for the nucleosomes and linker DNA. The modeled paths of the DNA linkers and the sites of the nucleosomes provide spatial constraints for positioning the globular core and modeling the folding of the disordered CTD of the linker histone. The pathways of the CTD are selected from ensembles of conformations obtained using ab initio structure prediction tools like Rosetta. We are using the model in coarse-grained Monte Carlo simulations of long-range interactions along arrays of precisely positioned nucleosomes in the presence of linker histones.